Writing

Topics

  • Markdown Syntax
  • Referencing

Markdown Syntax

When writing the body of your document, you will use the Markdown format.

Markdown is a lightweight markup language that you can use to add formatting elements to plaintext text documents. - Markdown Guide

Markdown

Introduction

Welcome to my awesome class. You will learn all kinds of useful things about R markdown.

Learning Markdown

You can familiarize yourself with Markdown in a couple of minutes using the following link: https://www.markdownguide.org/cheat-sheet/.

You can also use the Visual Editor in VS Code or RStudio, to see Markdown syntax previewed in it’s final format as you write. The Visual Editor also has some common Word-like shortcuts, such as Ctrl + B to make text bold.

Markdown Sneak Peek: Text Formatting

Markdown Syntax Output 
*italics* and **bold**
 italics and bold 
superscript^2^ / subscript~2~
 superscript2 / subscript2 
~~strikethrough~~
 strikethrough 
`verbatim code`
 verbatim code

Markdown Sneak Peek: Headers

Markdown Syntax Output 
# Header 1

Header 1

 
## Header 2

Header 2

 
### Header 3

Header 3

 
#### Header 4

Header 4

Markdown Sneak Peek: Lists

* unordered list
  + sub-item 1
    - sub-sub-item 1
  + sub-item 2
  • unordered list
    • sub-item 1
      • sub-sub-item 1
    • sub-item 2
1. ordered list
2. item 2
   i. sub-item 1
      A.  sub-sub-item 1
  1. ordered list
  2. item 2
    1. sub-item 1
      1. sub-sub-item 1
*   item 2
    
    Continued (indent 4 spaces)

  • item 2

    Continued (indent 4 spaces)

term
: definition
term

definition

Markdown Sneak Peek: Tables

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |
Right Left Default Center
12 12 12 12
123 123 123 123
1 1 1 1

Markdown Sneak Peek: Equations

  • Anything inside dollar signs $ is treated as “inline” maths
  • $$ is a standalone equation
  • Whitespace matters: $x$ is an equation, $x $ is not
  • Equations follow “LaTeX” rules

Equations are special

  • This \(x^2\) is inline

  • This equation is standalone \[\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_i\]

Markdown Sneak Peek: Callout blocks

  • Call-out blocks highlight sections of text that interrupt the flow of your regular text. Maybe it’s a definition, a warning, or a sidenote

  • When rendering your document to HTML, callout blocks are interactive and can be collapsed and opened.

    My First Callout Block!

    Say things here

Callout blocks

Note

Note that there are five types of callouts, including: note, tip, warning, caution, and important.

Callout blocks

Warning

Callouts provide a simple way to attract attention, for example, to this warning.

This is important

Danger, callouts will really improve your writing.

Tip with caption

Caution, under construction

Here is something under construction

Callout markdown syntax

Expand To Learn About Collapse

This is an example of a ‘folded’ caution callout that can be expanded by the user. You can use `collapse=“true”` to collapse it by default or `collapse=“false”` to make a collapsible callout that is expanded by default.

Exercise

  1. Go to the Writing/Reference section on the website and refer to the text provided in the Exercise section.

  2. Copy the text into your Quarto document, like an Introduction of sorts, and reformat it with Markdown Syntax

  3. Render the document to HTML.

10:00

Referencing

BibTex Keys

Now that we know how to write in Markdown, let’s add some references!

Adding reproducible references happens with BibTex keys. A typical BibTex key might look like as follows:

@article{nash51,
  author  = "Nash, John",
  title   = "Non-cooperative Games",
  journal = "Annals of Mathematics",
  year    = 1951,
  volume  = "54",
  number  = "2",
  pages   = "286--295"
}

Working With BibTex Keys

We will work with with bibliographies in the form of .bib files (BibTeX Bibliographical Database). .bib files are text files which contain a list of references in the form of BibTex keys.

Here is an example of another BibTex key for a reference used in this workshop:

@misc{RMarkdownWritingReproducible,
    title = {{RMarkdown} for writing reproducible scientific papers},
    url = {https://libscie.github.io/rmarkdown-workshop/handout.html},
    urldate = {2023-04-18},
    file = {RMarkdown for writing reproducible scientific papers:C\:\\Users\\Moope001\\Zotero\\storage\\SJITSZZI\\handout.html:text/html},
}

Working With BibTex Keys

The typical workflow is as follows:

  1. Find a reference that you need in your manuscript.
  2. Save it to your Zotero library via the browser extension
    Zotero automatically updates your .bib file through syncing with Zotero desktop and updating the .bib file.
  3. Cite the references using the @ + reference identifier:
    • In-text citations: @nash51 OR @RMarkdownWritingReproducible
    • Bracketed citations: [@nash51] OR [@nash51, @RMarkdownWritingReproducible]

More info: https://quarto.org/docs/authoring/footnotes-and-citations.html

Exercise

Go to the Referencing section on the website and refer to the instructions in the Exercise section.

You will go through the workflow of creating a .bib file that will be automatically updated by Zotero and integrating it with your Quarto document.

10:00

References on the fly

  • Alternatively, when using the Visual Editor option - you can use the citation dialog/option to insert citations directly.

  • Let’s go to RStudio!

APA Style

  • You need to use a csl (citation style guide) file to make sure references are properly formatted

  • I have included the apa7.csl file in the project folder

    • This will format references/citations in accordance with APA 7th edition

Exercise

  • Add the csl to your YAML and include the apa7.csl file

csl: apa7.csl

  • Render your document
02:00